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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGAGCGCCATGGCCAAGAGCTCGTTCAAGCTGGACCACACGCTCGgtcggtttgttttcttatcgtgttcctctttttattttttcctatatgtgctttagtagtgtggctgcgatgattgcgtgttgggtttatttgttcgata...

Basic information

species Oryza sativa
transcript LOC_Os04g53240.2
intron # 3
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86418393|gb|CI032602.1|CI032602
EST:     GAAGGAGCGCCATGGCCAAGAGCTCGTTCAAGCTGGACCACACGCTCG                         AGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAA
genomic: GAAGGAGCGCCATGGCCAAGAGCTCGTTCAAGCTGGACCACACGCTCGgtcggtttgt ... tgtatttcagAGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAA
EST: gi|33688345|gb|CF316584.1|CF316584
EST:     CAAGAGCTCGTTCAAGCTGGACCACACGCTCG                         AGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAA
genomic: CAAGAGCTCGTTCAAGCTGGACCACACGCTCGgtcggtttgt ... tgtatttcagAGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGAGCGCCATGGCCAAGAGCTCGTTCAAGCTGGACCACACGCTCGgtcggtttgttttcttatcgtgttcctctttttattttttcctatatgtgctttagtagtgtggctgcgatgattgcgtgttgggtttatttgttcgata

 AAGGAG
- - - - - - - - - AGAGCT
- - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - -  GCTGGA